# How to convert scRNA gene names to common gene IDs?

**URL:** <https://community.brain-map.org/t/how-to-convert-scrna-gene-names-to-common-gene-ids/723>\
**Category:** Transcriptomics Explorer\
**Tags:** analysis\
**Created:** [October 8, 2020, 3:54pm UTC](https://community.brain-map.org/t/how-to-convert-scrna-gene-names-to-common-gene-ids/723 "2020-10-08T15:54:07Z")\
**Posts on this page:** 3\
**Page:** 1

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**Author:** ![dg520](https://avatars.discourse-cdn.com/v4/letter/d/f0a364/32.png) [@dg520](https://community.brain-map.org/u/dg520)\
**Post date:** [October 8, 2020, 3:54pm UTC](https://community.brain-map.org/t/how-to-convert-scrna-gene-names-to-common-gene-ids/723/1 "2020-10-08T15:54:07Z")

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Hi all,

I’m using Allen Brain’s Human Cortex scRNA data as a reference set in my analysis. I’m trying to integrate my data with Allen Brain’s. However, I found the gene symbols used in Allen Brain’s data seems not compatible with mine (which is based on Ensembl GRCh38.92). Is there a way to convert Allen Brain’s scRNA gene symbols to common IDs (e.g. Ensembl gene ID, Genecode ID, etc)? And may I know which version of ID (e.g. GRCh38 version 100) they refer to?

Thanks a lot!

Best,  
Dadi

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**Author:** ![jeremyinseattle](https://yyz1.discourse-cdn.com/flex027/user_avatar/community.brain-map.org/jeremyinseattle/32/50_2.png) [@jeremyinseattle](https://community.brain-map.org/u/jeremyinseattle)\
**Post date:** [October 8, 2020, 4:26pm UTC](https://community.brain-map.org/t/how-to-convert-scrna-gene-names-to-common-gene-ids/723/2 "2020-10-08T16:26:04Z")

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Hi Dadi,

Information about the gene expression component of the Allen Cell Types Database is available in the “Transcriptomics Overview” [documentation](http://help.brain-map.org/display/celltypes/Documentation). For your question: “_For human, raw read files were aligned to the GRCh38 human genome sequence (Genome Reference Consortium, 2011) with the RefSeq transcriptome version GRCh38.p2 (current as of 4/13/2015) and likewise updated by removing duplicate Entrez gene entries from the gtf reference file._”

Regarding gene conversion, if you want to do this one gene at a time, I would suggest using [GeneCards](https://www.genecards.org/), where external IDs are listed near the top of the page for a given gene. If you want to do this for many genes at once, I would suggest [BioMart](http://www.biomart.org/), which has both a web portal and and R language library ([biomaRt](https://www.bioconductor.org/packages/release/bioc/html/biomaRt.html)) for gene ID conversion.

Best,  
Jeremy

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**Author:** ![dg520](https://avatars.discourse-cdn.com/v4/letter/d/f0a364/32.png) [@dg520](https://community.brain-map.org/u/dg520)\
**Post date:** [October 8, 2020, 4:36pm UTC](https://community.brain-map.org/t/how-to-convert-scrna-gene-names-to-common-gene-ids/723/3 "2020-10-08T16:36:43Z")

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Hi Jeremy,

Really appreciate your instruction. This is very helpful and I can work from here to convert all the gene names to the same reference.

Best,  
Dadi